tbuckley/cabot-search huggingface dataset:
METB-09. GERMLINE PATHOGENIC VARIANTS IN 838 PEDIATRIC BRAIN TUMOR PATIENTS
Authors: Shelly W McQuaid, Rebecca Kaufman, Ryan J Corbett, Zalman Vaksman, Miriam Bornhorst, Miguel A Brown, Yiran S Guo, Yuankun Zhu, Allison P Heath, Phillip B Storm, Adam C Resnick, Angela J Waanders, Kristina A Cole, Jo Lynne Rokita, Suzanne Macfarland, Sharon J Diskin
Journal: Neuro-Oncology (2023)

Abstract The genetic contribution of rare pathogenic germline variation in cancer patients without a family history remains unclear. We sought to characterize the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in pediatric brain tumor patients. Paired tumor and normal whole genome or exome sequencing was performed for 838 patients in the Pediatric Brain Tumor Atlas (PBTA). Rare variants in 196 CPGs were annotated as pathogenic (P) or likely pathogenic (LP) in an automated manner consistent with American College of Medical Genetics criteria and reviewed by an interdisciplinary panel. To assess enrichment, the frequency of CPG P-LP variants in cases was compared to the gnomAD v3.1 cancer-free control cohort (n=74,023). Second hit, mutational signature, and gene set enrichment analyses (GSEA) were performed on matched tumor sequencing to characterize differences in patients with and without germline P-LP variants in DNA repair genes. We observed 178 germline CPG P-LP variants in 163 PBTA patients (19.5%). CPG P-LP variants were most prevalent among Neurofibroma plexiform patients (64.3%), and NF1 and TSC2 harbored the most significant P-LP variant burden compared to controls (OR=69.5, p=2.4E-23, CI=34.6-137 and OR=357, p=1.1E-14, CI=71-3669, respectively). DNA repair gene P-LP variants were enriched in cases compared to controls (OR=4.4, p=8.3E-30). Patients harboring mismatch repair (MMR) gene P-LP variants exhibited significantly higher tumor-associated MMR-deficiency mutational signature exposures (p&amp;lt;0.05) and DNA repair GSEA scores relative to other patients (p=0.04). Second hit SNVs in tumors were identified in four patients with P-LP germline variants in NF1 (n=2), APC (n=1), and SUFU (n=1). Germline P-LP variants are enriched in PBTA patients, and DNA repair variants are predictive of repair-deficiency signatures in tumor samples. Our work emphasizes the need for germline sequencing to inform patient care.
DIPG-35. IDENTIFYING DRIVER-SPECIFIC VULNERABILITIES IN PAEDIATRIC HIGH GRADE GLIOMA SUBTYPES
Authors: Antonella De Cola, Michael McNicholas, Amelia Foss, Cameron Lloyd, Steven Hébert, Damien Faury, Augusto Faria Andrade, Nada Jabado, Claudia Kleinman, Manav Pathania
Journal: Neuro-Oncology (2023)

Abstract Paediatric high-grade gliomas (pHGGs) are incurable malignant brain tumours and a leading cause of cancer-related death in children. The majority of pHGGs carry lysine-to-methionine (K27M) or glycine-to-arginine/valine (G34R/V) mutations in histone variants H3.1 or H3.3. Moreover, histone mutations associate with different anatomical locations and co-segregating mutations defining distinct tumour subtypes within pHGG. However whether these co-occuring mutations can act as drivers to modify tumour phenotypes and drug sensitivities is currently unknown. In order to functionally evaluate the role of partner alterations and to identify new therapeutic targets, we developed in vivo tumour models of pHGG subtypes using in utero electroporation (IUE) in combination with piggyBac transposon and CRISPR technology. We also established ex vivo glioma stem cell (GSCs) lines from mouse models with different co-segregating mutations, able to engraft in syngeneic immune-competent mice. Then, we performed transcriptome analysis and drug screening identifying selective pharmacological vulnerabilities. Our approach represents a preclinical platform to evaluate subtype-specific precision therapies identifying new pathways involved in brain tumour initiation, progression and maintenance.
HGG-25. TARGETED DRUGS SYNERGIZE WITH DOUBLE ALKYLATOR THERAPY IN H3.3 G34R/V PEDIATRIC HIGH-GRADE GLIOMA
Authors: Rebecca Haase, Adam Green, Lindsay Kilburn, Mariella Filbin
Journal: Neuro-Oncology (2023)

Abstract Diffuse hemispheric H3 G34R/V mutant gliomas (G34R/V DHG) are lethal brain malignancies occurring in the cerebral hemisphere of adolescent patients with no effective treatment options. To date, standard care is adapted from adult treatment protocols which include maximal tumor resection, radiotherapy, and chemotherapy with temozolomide (TMZ). In a recent study led by the Children’s Oncology Group (COG, ACNS0423), the combination of the alkylators TMZ and lomustine (CCNU) showed improved event-free survival for pediatric high-grade glioma patients. Still, patient benefits remain limited and thus demand further improvement of treatment protocols. Therefore, the aim of this study is to identify FDA-approved blood-brain-barrier crossing compounds that specifically targeting known vulnerabilities of pediatric high-grade glioma that achieve synergistic treatment results when combined with the double alkylator approach. We conducted a compound screen in combination with TMZ and CCNU on G34R/V-tumor derived gliomaspheres to identify synergies based on cell viability assays in vitro. We identified three candidate agents - Fimepinostat, trametinib, and avapritinib, which inhibit different key oncogenic targets in pediatric high-grade glioma - Pi3K and histone-deacetylases, MAPKs, and PDGFRA, respectively. Our ongoing in vivo study elaborates the translatability of the identified combinatorial therapies in patient derived G34R/V DHG orthotopic xenograft models. We are comparing different study arms of single agent treatment and double as well as triple combinations of alkylators and the candidate agents. This study will serve to determine (i) treatment efficacy, as measured by tumor growth and survival, (ii) occurring side effects, especially alkylator-induced suppression of platelet counts, and (iii) molecular changes upon different treatments using single cell transcriptomics and immunohistochemistry. In summary, we present valuable pre-clinical data supporting the combination of alkylators with targeted agents as a novel treatment strategy in G34R/V DHG, which might be translated into a promising strategy of a new comparative study based on COG trial ACNS0423.
BIOL-08. RADIATION DRIVES METASTASIS IN MEDULLOBLASTOMA THROUGH AN INFLAMMATORY PROCESS
Authors: Carolina Nor, Kaitlin Kharas, Alexandra Rasnitsyn, Maria Vladoiu, Vijay Ramaswamy, David Raleigh, Michael Taylor
Journal: Neuro-Oncology (2023)

Abstract Current treatment for medulloblastoma is comprised of surgery, radiotherapy (RT) and/or chemotherapy. Although the primary tumor is controlled with this approach, recurrent metastatic disease is ubiquitously fatal. However, little is known about the biology of metastatic recurrences in medulloblastoma. In the present study, we observe across 3 non-overlapping cohorts of infant medulloblastoma that patients recur locally without focal RT and metastatically after focal RT. Using 3 independent murine flank xenograft medulloblastoma models, we found that the incidence of leptomeningeal metastasis was significantly increased in mice that received RT compared to sham controls. We have also found a significant increase in viable circulating tumor cells after RT. Our multi-omics (bulk RNA-seq, scRNA-seq and proteo/phosphoproteomics) approach using immunocompetent sporadic medulloblastoma models treated with RT showed activation of the innate inflammatory response through the overexpression of chemokines, cytokines and activation of immune cell types. In situ analysis of protein expression after RT showed a gradual increase in the abundance of macrophages, neutrophils and dendritic cells after RT, suggesting increased permeability and cell trafficking across the blood brain barrier. Applying live intravital microscopy using a low molecular weight vascular dye (150kDa), we observed a striking increase in blood vessel permeability in RT vs sham-treated brain tumors. Our observations support a model where RT drives metastasis through inflammation. To test this, we applied lipopolysaccharide (LPS), an inflammation inducing treatment, to a sporadic murine medulloblastoma model which significantly increased the metastatic burden. We then treated a xenograft model with dexamethasone in combination with RT, which resulted in total abrogation of metastatic dissemination compared to RT alone. Collectively, our findings suggest that while external beam irradiation is an effective and essential treatment for medulloblastoma, it may facilitate metastatic dissemination through an inflammation-induced process. These findings can help inform potential approaches to prevent disseminated relapsed disease.
DIPG-29. A CONNECT CONSORTIUM PRECLINICAL STUDY IDENTIFIES MEK INHIBITION AND RADIATION AS POTENTIAL COMBINATION PARTNERS FOR THE ALK2 INHIBITOR TP-0184 IN ACVR1-MUTANT DMG
Authors: Rebecca Rogers, Maria Tsoli, Shiva Senthil Kumar, Elisabet Fernandez Potente, Matt Biery, Yura Grabovska, Alan Mackay, Diana Carvalho, Rita Pereria, Anna Burford, Drenusha Sejdiu, Ruth Ruddle, Florian Gabel, Florence Raynaud, Sridevi Yadavilli, Sean Mizoguchi, Bavani Subramaniam, Lindsey Kilburn, Eugene Hwang, Javad Nazarian, Nicholas Vitanza, David Ziegler, Rachid Drissi, Chris Jones
Journal: Neuro-Oncology (2023)

Abstract Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant orthotopic xenografts with multiple chemotypes of ALK2 inhibitors (ALK2i) results in extended survival in vivo but, as single agents, these inhibitors are unable to achieve a complete anti-tumour response. To identify novel combination strategies alongside ALK2 inhibition, five international laboratories pooled resources to evaluate the ALK2i TP-0184 across 26 patient-derived DMG-H3K27 models in vitro, demonstrating GI50 values of ~0.5-10uM, although with no significant difference between ACVR1-mutant and wild-type. Genome-scale CRISPR screens of ALK2i-treated ACVR1-mutant models revealed specific genetic dependencies in critical nodes of several signalling pathways including MTOR, as well as PPP2R1A, known to play a role in MAPK pathway activation. Biomarker analysis showed inhibition of phospho-SMAD1/5/9 by western blot, with RNAseq and proteomic analysis indicating downstream signalling consequences in BMP/SMAD signalling following TP-0184 treatment. We observed synergistic pharmacological interactions between TP-0184 and both everolimus (mTORi) and trametinib (MEKi) in 7 to 8 ACVR1-mutant DMG models, respectively, with the latter validated across laboratories using orthogonal assays. Importantly, combining TP-0184 with radiation in vitro showed a profound radiosensitisation effect of the ALK2i in three ACVR1-mutant models using both clonogenic and cell viability assays in multiple laboratories, in part due to an observed activation of phospho-SMAD1/5/9 by radiation. Finally, in vivo tolerability and pharmacokinetic assays in multiple immuno-compromised and immune-competent mouse strains suggested a dose of 150mg/kg TP-0184 and 0.4mg/kg trametinib for use in in vivo efficacy studies, with good CNS penetrance of both drugs in excess of in vitro GI50 values. Such studies have been initiated in six DMG-H3K27 models across our laboratories to robustly assess the combination of TP-0184 and trametinib/radiation to support rapid potential translation to clinical trial.
LGG-14. TREATMENT OF TWO PEDIATRIC FGFR-ALTERED LOW-GRADE GLIONEURONAL TUMORS WITH MEK INHIBITION
Authors: Margot Lazow, Diana Thomas, Catherine Cottrell, Daniel Kobolt, Swetha Ramadesikan, Ralph Salloum, Ammar Shaikhouni, Elaine Mardis, Jeremy Jones, Jeffrey Leonard, Daniel Boué, Maryam Fouladi, Kathleen Schieffer
Journal: Neuro-Oncology (2023)

Abstract Somatic alterations in the fibroblast growth factor receptor (FGFR) gene family (FGFR1/2/3) have been implicated in tumorigenesis across pediatric low-grade glioneuronal neoplasms and represent a potential therapeutic target. FGFR rearrangements and internal tandem duplication (ITD) cause constitutive receptor tyrosine kinase activation, thereby promoting tumor cell growth, differentiation, and survival through complex downstream signaling, including via the mitogen activated protein kinase (MAPK) pathway. With increasing safety and efficacy data in pediatric neuro-oncology, MEK inhibitors may be considered to target MAPK pathway activation in FGFR-altered low-grade glioneuronal tumors, although clinical evidence within this specific molecular subgroup is lacking. Herein, we describe two cases of pediatric low-grade glioneuronal tumors harboring FGFR aberrations with encouraging clinical and radiographic response to MEK inhibition. The first patient has a multiply recurrent left parietal dysembryoplastic neuroepithelial tumor (DNET) with an FGFR1 ITD, diagnosed at eight years of age after presenting with seizures. Despite two surgical resections (with identical pathology), his disease slowly progressed. Oral MEK inhibitor therapy with trametinib was initiated, which he has remained on for the past 9+ months, with stable residual tumor without continued radiographic progression. The second patient was diagnosed at three years of age with focal epilepsy, prompting imaging demonstrating an infiltrative T2/FLAIR-hyperintense right temporal mass. Subtotal resection was performed, with pathology consistent with pediatric-type diffuse low-grade glioma. Molecular profiling identified an FGFR3-TACC3 fusion, with suspected enrichment for MAPK-pathway activation by preliminary RNA-sequencing analyses. Adjuvant therapy with trametinib was started, with small reduction in residual disease burden observed radiographically three months into treatment. Both patients continue on MEK inhibitor therapy with minimal toxicity and adequate control of underlying seizures. Though further research in larger, prospective cohorts with comprehensive biology data is necessary, oral MEK inhibitors represent a feasible and rational treatment consideration for pediatric FGFR-altered low-grade glioneuronal tumors.
DIPG-22. TRIPTOLIDE AS A POTENTIALLY PROMISING THERAPY FOR DIFFUSE MIDLINE GLIOMA
Authors: Ludovica Ciani, Sandra Laternser, Bettina Kritzer, Kerstin Hasler, Justyna M Przystal, Mohana R Velagapudi, Marta M Alonso, Marta Zalacain, Sabine Müller, Javad Nazarian
Journal: Neuro-Oncology (2023)

Abstract Diffuse Midline Gliomas (DMG) are amongst the most lethal pediatric brain tumors. Children diagnosed with DMG face a grim prognosis of 9-11 months from diagnosis. Over 85% of DMG patients harbor mutation affecting histone-encoding genes (H3.1K27M, H3.3K27M) leading to genome hypomethylation and transcriptional disruption. Despite decades of clinical studies, the development of an effective therapy remains a challenge. Triptolide is a diterpenoid triepoxide compound inhibiting cell growth and exhibiting preclinical antitumor activity. A large drug screen conducted by the NCI using DMG cell lines identified triptolide as a candidate for reducing DMG cell viability. To further investigate triptolide and its potential for clinical intervention, we used DMG preclinical in vitro and in vivo models. In vitro viability assays with triptolide alone and in combination with other therapeutic drugs (ONC201 and ONC206), were carried out using seven DMG cell lines. Single treatment with triptolide resulted in a significant decrease in DMG cell viability and combination with both ONC201 and ONC206 showed additivity. Triptolide’s toxicity was assessed in vivo through direct injections into the yolk sac of zebrafish. Preliminary data demonstrated how triptolide has higher toxicity compared to un-injected and DMSO control groups. However, a major limitation of triptolide’s clinical utility is its low solubility. Therefore, for in vivo studies, we used minnelide, a water-soluble analog of triptolide, with potent antitumor properties. Studies were performed in eleven RAG2 female mice. PDX tumor-bearing mice were treated with minnelide and ONC201 for three weeks as single or in combination. Survival studies showed no significance in minnelide monotherapy. However, minnelide + ONC201 combination therapy resulted in significant (p=0.01) survival of PDX models. Our current studies investigate the efficacy of a higher dose of minnelide in vivo. Our goal is to establish minnelide potential as a combination strategy for the treatment of children diagnosed with DMG.
NCCN Virtual Policy Summit: Defining the “New Normal” — 2021 and the State of Cancer Care in America Following 2020
Authors: Alyssa A. Schatz, Lindsey Bandini, Robert W. Carlson
Journal: Journal of the National Comprehensive Cancer Network (2023)

Abstract US healthcare systems have been deeply impacted by significant societal shifts over the past several years. The COVID-19 pandemic has changed the way we interact with healthcare, political narratives have impacted how healthcare is perceived and engaged with by the public, and the United States has become increasingly aware of historic and ongoing racial injustices across all health and social systems. The watershed events experienced during the last several years play a critical role in shaping the future of cancer care for payers, providers, manufacturers, and, most importantly, patients and survivors. To explore these issues, in June 2021 NCCN convened a virtual policy summit: Defining the “New Normal” — 2021 and the State of Cancer Care in America Following 2020. This summit offered the opportunity for a varied group of stakeholders to begin to explore the impact of recent events on the current and future state of oncology in the United States. Topics included the impact of COVID-19 on cancer detection and treatment, the role of innovation in ensuring continuity of care, and efforts to create more equitable systems of care.
IMG-10. MAGNETIC RESONANCE FUNCTIONAL IMAGING BIOMARKER FOR DISTINGUISHING HIGH GRADE FROM LOW GRADE PEDIATRIC BRAIN TUMORS
Authors: Teresa Gross Kelly, Kathleen Schmainda, Melissa Prah, Knipstein Jeffrey, Mohit Maheshwari, Sean Lew, Marjorie Bessette Baker
Journal: Neuro-Oncology (2023)

Abstract This study aims to show that the ratio between perfusion MRI (RCBV) and diffusion MRI (ADC - apparent diffusion coefficient) is more effective in distinguishing low-grade from high-grade pediatric brain tumors than either parameter (RCBV or ADC) alone. After IRB approval was obtained, an initial pilot prospective study was performed that included 38 patients (newborn - 18 years) (22 females and 16 males). All MRI exams were performed on a 1.5 T or 3.0 T scanner. Surgically resected tumors were classified as low grade (WHO I, II) or high grade (WHO III, IV). ROIs were selected using tumor boundaries delineated on the FLAIR sequence, excluding perilesional edema. Both standardized and normalized perfusion RCBV (sRCBV, nRCBV) as well as diffusion (ADC) mean values were acquired. Then sRCBV/ADC ratios were calculated. Statistical analysis included the Wilcoxon-Mann-Whitney t-test using an alpha=0.05 as the level of significance. The results of this preliminary study revealed that the sRCBV/ADC ratio calculations were more effective at separating high grade from low grade tumors than were RCBV or ADC values alone. As a result of this original pilot study, the calculated sRCBV/ADC ratio has occasionally been used as a clinical tool at our institution. In order to validate the results from this original pilot study, we have collected additional retrospective data to increase sample size. We plan to share the results of this additional data in order to validate that the sRCBV/ADC ratio is an easy-to-use imaging biomarker that can effectively separate high grade from low grade pediatric brain tumors. This information is useful for patient care in that it can potentially help predict prognosis which is essential for parental counseling, and potentially reduce the need for invasive tests and biopsies.
MDB-16. TARGETING EPIGENETIC DYSREGULATION IN PAEDIATRIC BRAIN TUMOURS
Authors: Sara Badodi, Silvia Marino
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB) is the most common paediatric malignant brain tumour and is classified into four distinct molecular subgroups (WNT, SHH, G3 and G4), each of them further divided into subtypes with different prognosis and responses to therapy. Deregulation of chromatin modifier genes play an essential role in MB, particularly in the G4 subgroup. A BMI1High;CHD7Low molecular signature identifies patients with poor survival. We have shown that BMI1High;CHD7Low sustains MB growth through regulation of MAPK/ERK signalling and via epigenetic regulation of inositol metabolism in both G4 MB cells and patients. These tumours display over-activation of MAPK/ERK and AKT/mTOR pathways leading to energetic rewiring characterised by enhanced glycolytic capacity and reduced mitochondrial function. We demonstrate that inositol administration counteracts this metabolic alteration and significantly extends survival in an in vivo pre-clinical model. Additionally, we identify a synergistic vulnerability of G4 MB to a combination treatment with BMI1 and MAPK/ERK inhibitors that overcomes the acquired resistance induced by single drug therapies. Importantly, we have now analysed recurrent G4 MB and found that the BMI1High;CHD7Low signature is maintained at recurrence and it continues to predict the pharmacological vulnerabilities we previously described. Finally, we extended the analysis to other paediatric brain tumours, including histone mutant gliomas and ependymomas, and identified molecularly defined subgroups that exhibit differential response to the compounds predicted to be effective by the BMI1High;CHD7Low signature, hence expanding the spectrum of tumour potentially amenable to these novel pharmacological approaches.